Package: R.oo
=============
Version: 1.19.0 [2015-02-27]
o Now charToInt() returns integers as documented (was numerics).
o ROBUSTNESS: Now explicitly declare "default" S3 methods for
getClasses and getMethods.
o ROBUSTNESS: Dropped non-ASCII characters from R source comments.
o BUG FIX: objectSize() for environment could result in infinite
recursive calls if there circular dependencies between environments.
Added package test for objectSize() including this case.
o BUG FIX: getKnownSubclasses() for Class could throw an error if one
of the objects "scanned" for being a function and of class Class
would thrown an error from just looking at it. See R-devel thread
'Inspect a "delayed" assigned whose value throws an error?'
on 2015-01-26 for details.
o BUG FIX: Forgot to explicitly import getClasses and getMethods from
the 'methods' package. Interestingly, this one has never given an error.
o BUG FIX: getStaticInstance() for Object now searches the parent/calling
environment as well. This covers the case when constructors and objects
are created in a local environment (contrary to package namespaces and
the global environment).
Version: 1.18.5 [2015-01-05]
o CLEANUP: Now update() for Package is defunct; use update.packages().
Version: 1.18.4 [2014-12-29]
o Added argument 'decreasing' to ll(), e.g.
ll(sortBy="objectSize", decreasing=TRUE).
Version: 1.18.3 [2014-10-18]
o BUG FIX: Rdoc$compile() and Rdoc tag @allmethods failed to provide
links and titles on non-exported S3 methods.
Version: 1.18.2 [2014-04-26]
o Now Rdoc$getRdUsage() escapes '%*%' to `'\%*\%'` in the Rd output.
Version: 1.18.1 [2014-03-30]
o BUG FIX: Now getRdDeclaration(), getRdHierarchy() and getRdMethods()
for Class handles also non-exported methods and Classes.
Version: 1.18.0 [2014-02-22]
o IMPORTANT: A registered finalizer function for Object:s no longer
calls finalize() on the Object itself unless the R.oo package is
loaded, whereas previously it would have tried to temporarily reattach
the R.oo package. On the other hand, it is now sufficient to have
R.oo loaded for finalize() to be called, whereas in the passed it also
had to be attached.
o DEPRECATED: Deprecated gc() for Object. Use clearCache(..., gc=TRUE)
instead.
Version: 1.17.1 [2014-02-05]
o CLEANUP: Argument 'properties' of ll() defaults to an options, which
if not set in turn defaults to a given value. The ll() method is no
longer trying to set that option if missing. The option is also no
longer set when the package is attached.
Version: 1.17.0 [2014-01-05]
o Now Class$forName() searches all loaded namespaces as a last resort.
Version: 1.16.2 [2014-01-05]
o Now static method Class$forName() accepts optional 'envir'
argument for specifying from where to search for the Class object.
o Added argument 'gc=FALSE' to clearCache(). It is recommended
to start using clearCache(obj, gc=TRUE) instead of gc(obj).
o CLEANUP: Defunct registerFinalizer() for Object.
o BUG FIX: The temporary finalizer() registered for Object while
loading the R.oo package itself would cause cyclic loading of R.oo.
The reason was that it checked whether R.oo was available or not,
by only looking at attached namespaces but not loaded ones. This
bug was introduced in R.oo 1.16.0.
o Bumped package dependencies.
Version: 1.16.1 [2014-01-04]
o ROBUSTNESS: Added several missing importFrom() and S3method()
statements to the NAMESPACE file.
Version: 1.16.0 [2013-10-13]
o ROBUSTNESS: Added argument 'finalize' to Object() to specify
whether a finalizer should be registered or not. If so, then
generic function finalize() is called on the Object.
Furthermore, extend() for Object gained argument '...finalize',
which, regardless of argument 'finalize' of Object, force the
registration of a finalizer (...finalize=TRUE) or the removal
of one (...finalize=FALSE). If ...finalize=NA (default), then
the finalizer is enabled/disabled according to argument
'finalize' of Object. For backward compatibility reasons, the
default behavior is still to register a finalizer for Object:s,
but this may change in a future release.
o ROBUSTNESS: Now the package's system tests assumes that it's
only the 'base' package that is attached.
o BUG FIX/ROBUSTNESS: Now Object finalizers will no longer try to
re-attach the 'R.oo' package if library() is in the process of
trying to attach another package, because otherwise a cyclic
loading of namespaces may occur. This was observed for a package
that allocated a temporary Object .onAttach() which then was
garbage collected and finalized.
Version: 1.15.8 [2013-10-10]
o BUG FIX/ROBUSTNESS: It appears that when loading the package
it may happen that the 'R.oo' namespace is loaded cyclicly,
though this has only been observed while running 'R CMD INSTALL'.
This may be because a Package object (R.oo::R.oo) is assigned
during the loading of the namespace. Since Package extends()
an Object object, this may end up loading 'R.oo' again. To
avoid this, R.oo::R.oo is now assigned using delayed assignment.
Version: 1.15.7 [2013-10-08]
o ROBUSTNESS: Now using inherits=FALSE in several internal
exists()/get() calls.
Version: 1.15.6 [2013-10-07]
o Now importing getCall() from 'stats', iff R (>= 2.14.0).
o Now Rdoc tag @howToCite does a better job when there are
multiple citations in CITATION.
Version: 1.15.5 [2013-09-28]
o Now the 'R.oo' Package object is also available when the
package is only loaded (but not attached).
Version: 1.15.4 [2013-09-26]
o CLEANUP: Deprecated update() for Package.
o CLEANUP: Deprecated non-used registerFinalizer() for Object.
Version: 1.15.3 [2013-09-23]
o Now properly declaring all S3 methods in the NAMESPACE file.
Version: 1.15.2 [2013-09-20]
o ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs().
o BUG FIX: The finalizer function registered by extend() for Object:s
assumed that the 'utils' is attached while calling capture.output(),
which under certain conditions could generate 'Error in
getObjectInfo(this) : could not find function "capture.output"'
while the garbage collector was running. In extreme cases it could
also crash R.
Version: 1.15.1 [2013-08-29]
o library("R.oo", warn.conflicts=FALSE, quietly=TRUE) will load the
package completely silently.
o Now startupMessage() for Package acknowledges library(..., quietly=TRUE).
o setConstructorS3() no longer requires that R.oo is attached ("loaded").
Version: 1.15.0 [2013-08-23]
o CLEANUP: Dropped deprecated inst/HOWTOSITE replaced by inst/CITATION.
o CLEANUP: Package no longer utilizes ':::'.
o CLEANUP: Made get- and showHowToCite() protected methods.
o CLEANUP: Now getHowToCite() for Package utilizes utils::citation(),
if package don't contain a HOWTOCITE file. It is recommended to
write packages with CITATION instead of HOWTOCITE.
o CLEANUP: Hiding non-essential methods from the Rd help index, e.g.
charToInt(), intToChar(), hashCode(), equals(), dimension() and trim().
Version: 1.14.0 [2013-08-20]
o Now it's possible to call static methods without attaching
("loading") the package, e.g. R.oo::Class$forName("Object").
Added unit tests for this.
o Now getPackage() for Class first searches the namespace of the
Class object and then the attached ("loaded") packages.
o Now '$' and '$= 2.15.2 Patched r61487).
Version: 1.11.6 [2013-01-08]
o Added argument 'format' to getInternalAddress() for Object.
o BUG FIX: The hexadecimal string returned by as.character() for
Object would contain the decimal value and not the hexadecimal one.
Version: 1.11.5 [2012-12-28]
o GENERALIZATION: Further preparation for supporting R.oo and its
derived packages to be imported without attaching ("loading") them.
o Replaced all data.class(obj) with class(obj)[1L].
o ROBUSTNESS/BUG FIX: getMethods() for Class would give an error if
no methods were found for the queried Class.
o ROBUSTNESS/BUG FIX: In the rare case where getStaticInstance() for
Class failed to setup a static instance, the temporary state set
internally would not be unset.
Version: 1.11.4 [2012-12-19]
o Added startupMessage() for Package.
Version: 1.11.3 [2012-12-18]
o R CMD check for R devel no longer gives a NOTE on attach().
Version: 1.11.2 [2012-11-29]
o Made getKnownSubclasses() for Class a bit faster.
Version: 1.11.1 [2012-11-28]
o LIMITATION: Registered finalizer for pure Object:s (i.e. excluding
those which are of a subclass of Object) will no longer be called
if the R.oo package has been detached. This should be a very
unlikely scenario.
o BUG FIX: extend() for Object dropped existing field modifiers.
Version: 1.11.0 [2012-11-23]
o GENERALIZATION: Preparing for better support for Object/Class
in import-only namespaces, i.e. without packages being loaded.
o Now getStaticInstance() for Class sets the environment for the
returned Object to that of the Class.
Version: 1.10.3 [2012-11-18]
o ROBUSTNESS: Now nearly all S3 methods are declared properly in
the namespace.
o Updated the URL returned by RccViolationException$getRccUrl().
Version: 1.10.2 [2012-11-07]
o BUG FIX: obj$(...) would throw an error iff the Object 'obj'
was saved/instantiated by R.oo (< 1.10.0). Code is now backward
compatible with this case. Thanks Roger Day at University of
Pittsburgh Cancer Institute and Dan Tenenbaum (BioC core) for
reporting on this.
Version: 1.10.1 [2012-10-16]
o ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf.
R-devel thread 'Do *not* pass '...' to NextMethod() - it'll do it
for you; missing documentation, a bug or just me?' on Oct 16, 2012.
Version: 1.10.0 [2012-10-14]
o GENERALIZATION: Now $(...) calls the corresponding
generic function (static, ...), where 'static' is the
static object of Class . This allows for using NextMethod()
in static functions. Calls to $(...) and
$(...) were adjusted analogously.
o Now throw() for Exception outputs the error message both above and
below the stack trace, which is particularly useful when the stack
trace is long.
o BUG FIX: The stacktrace details collected by Exception dropped
the names of the functions.
Version: 1.9.10 [2012-09-14]
o ROBUSTNESS/BUG FIX: The Exception constructor could generate warning
'In if (regexpr("^function\\(", code) != -1) return("") : the
condition has length > 1 and only the first element will be used'
occurring in its local fcnName() function. Now code no longer assumes
that 'code' is of length 1.
Version: 1.9.9 [2012-09-11]
o Now throw() for Exception aborts (after signalling and outputting
the message) by calling stop(). Ideally it should utilize abort(),
but the new version of abort() may be "caught" is certain cases.
o ROBUSTNESS/CRAN POLICY: Updated abort() for condition to utilize
invokeRestart("abort"). This avoids having to call
.Internal(.signalCondition(...)). It also means that the message
outputted by abort() no longer starts with a "Error in ...:" line.
abort() imitates how stop() works but without the signalling.
o BUG FIX: getContribUrl() and getDevelUrl() would give an error if
corresponding fields did not exists in the DESCRIPTION file. Now
they return NAs just as getUrl().
Version: 1.9.8 [2012-06-22]
o GENERALIZATION: Added newInstance() for BasicObject.
o ROBUSTNESS: Now constructor BasicObject() is guaranteed to
return an object with non-duplicated class attribute elements.
Version: 1.9.7 [2012-06-20]
o CLEANUP: Dropped non-used adjusted getClass() generic function,
which means that now there is one less function masking the
'methods' package.
o BUG FIX/GENERALIZATION: throw() for Exception would give an error on
R < 2.14.0, where no generic getCall() exists. Now it works for
all versions of R.
Version: 1.9.6 [2012-06-11]
o BUG FIX/GENERALIZATION: Rdoc$getKeywords() now uses system
environment variable R_DOC_DIR for locating the internal
KEYWORDS.db. Thanks Charles Hogg at NIST for suggesting this.
Version: 1.9.5 [2012-04-20]
o Added argument 'export' to setConstructorS3().
o Now Rdoc$getUsage() searches also the package namespace for
the function/method definition. This is done, before looking
in the global search path.
o CLEANUP: setConstructorS3() no longer sets attribute "formals". It
has been deprecated since April 2003.
Version: 1.9.4 [2012-04-05]
o Now package imports and exports getCall() from the 'stats' package
so that generic function getCall() is available for Exception:s
also when 'stats' is not loaded, e.g. during executing .Rprofile.
Version: 1.9.3 [2012-03-18]
o Now it is possible to set the default value of argument 'cleanup'
of getStackTrace() for Exception via an option.
Version: 1.9.2 [2012-03-08]
o Made stack traces of Exception:s more informative and cleaner.
o Now the default throw() of R.methodsS3 is "quietly" overwritten,
i.e. there is no longer a warning about it when R.oo is loaded.
o Now package no longer warns about renaming existing functions
getMethods() and getClasses() of 'base' to default methods during
installation, iff R.methodsS3 (>= 1.2.3).
Version: 1.9.1 [2012-03-05]
o CLEANUP: throw() for 'error' is now just a wrapper for stop().
Previously it had to do what stop() now does for 'condition' objects.
o CRAN POLICY: Replaced all appendVarArgs() for 'base' functions that
do .Internal() calls, because they would then appear as local functions
of this package and hence not be accepted by CRAN according to their
new policies. Instead we now create "default" functions that are
wrappers to the corresponding functions in the 'base' package.
Extra care has to be taken for functions that have arguments whose
values are dependent on the call environment/closure.
o CRAN POLICY: Dropped .Internal() calls in the default ll() method,
in getMethods() for Class objects, and in throw() for Exceptions.
Version: 1.9.0 [2012-02-23]
o Now the package imports 'utils' instead of depending on it.
This means that all packages that depends on 'R.oo' for loading
'utils' for them need to explicitly load it themselves.
o The R.oo package now requires (at least) R v2.4.0 (Oct 2006!)
Version: 1.8.3 [2011-11-01]
o CLEANUP/FIX: Dropped package.description() from getDescriptionFile()
for Package, which was done for compatibility reasons when it was
deprecated in R v1.9.0. It will be dropped completely in R v2.15.0.
Version: 1.8.2 [2011-08-25]
o DOCUMENTATION: Added further clarification to help(setConstructorS3)
about the requirement that constructors defined by setConstructorS3()
have to be callable without arguments.
Version: 1.8.1 [2011-07-10]
o Changed first argument of getCall() to 'x', because that is what
the new getCall() method of 'stats' in R v2.14.0 uses.
Version: 1.8.0 [2011-04-03]
o ROBUSTNESS: Now finalizers for Object:s are registered to be called
also when the R session is quit, if the "R.oo::Object/finalizeOnExit"
option is TRUE. If FALSE (default), as before, the finalizers were
only executed when Object:s were cleaned up by the garbage collector.
o Turned of the default instantiation timestamp for Object and
BasicObject. The main reason is that it makes it very complicated
to calculate reproducible checksums. However, for backward
compatibility, it is possible to turn on the timestamp by setting
option "R.oo::Object/instantiationTime". For BasicObject there is
option "R.oo::BasicObject/instantiationTime".
o Added protected getFieldModifiers() and getFieldModifier().
o Added argument 'recursive' to clearCache() for recursively traversing
all elements are clearing the cache of all detected Object:s.
o Now clearCache() also calls clearLookupCache().
o Added protected clearLookupCache() for clearing internal objects
stored in the Object and that are used for faster field lookups.
o CLEANUP: Dropped deprecated getInstanciationTime().
Version: 1.7.5 [2011-02-01]
o ROBUSTNESS: Now using 'inherits' (not 'inherit') in all calls to
get() and exists().
Version: 1.7.4 [2010-09-22]
o Now Rdoc lines are allowed to start with double ('##') or triple
('###') comment characters in addition to single ('#') ones.
Version: 1.7.3 [2010-06-04]
o Now argument 'addTimestamp' of Rdoc$compile() defaults to FALSE.
This way the generate Rd file will remain identical unless there
are real Rdoc/code changes. Not adding timestamps is better when
working with a version control systems.
o BUG FIX: If there are no Rd files, then check() of Rdoc would
throw the error "object 'res' not found".
Version: 1.7.2 [2010-04-13]
o BUG FIX: Package(pkg) would throw "Error in Package(pkgname) : object
'package' not found", if 'pkg' is installed in multiple libraries.
Version: 1.7.1 [2010-03-17]
o CLEAN UP: Loading the package would generate warnings of
of several conflicts. Forgot to export '.conflicts.OK'
after adding the name space.
Version: 1.7.0 [2010-03-13]
o Added a NAMESPACE.
Version: 1.6.7 [2010-01-21]
o Added some more "get started" help to help(R.oo).
Version: 1.6.6 [2009-11-19]
o Added isOlderThan() for Package.
Version: 1.6.5 [2009-10-30]
o ROBUSTIFICATION: Lowered the risk for save() of Object to leave an
incomplete file due to say power failures etc. This is done by
first writing to a temporary file, which is then renamed. If the
temporary file already exists, an exception is thrown.
Version: 1.6.4 [2009-10-27]
o Removed a stray print() statement in attachLocally() for Object:s.
Version: 1.6.3 [2009-10-26]
o Added objectSize() for environments.
o BUG FIX: Rdoc$compile() did not work with R v2.10.0 and newer.
Version: 1.6.2 [2009-10-16]
o Some cleanup of Rd files to meet the stricter requirements.
Version: 1.6.1 [2009-10-09]
BUG FIX: getBundle() of Package gave "Error in getBundle.Package(pkg) :
subscript out of bounds" starting with R v2.10.0.
Version: 1.6.0 [2009-10-02]
o Added the Interface class, which is in an alpha version.
Version: 1.5.0 [2009-09-09]
o Fixed broken/missing Rd links.
Version: 1.4.9 [2009-07-07]
o Added protected method registerFinalizer() for Object.
Version: 1.4.8 [2009-05-18]
o DOC FIX: The titles for intToChar() and charToInt() where mixed up.
Thanks to Jens Philip Hoehmann for reporting this.
Version: 1.4.7 [2009-01-10]
o FIXUP: There were some Rd warnings with the new R v2.9.0.
Version: 1.4.6 [2008-08-11]
o Replaced all 'a %in% b' with is.element(a,b) due to an old and
weird bug that I cannot reproduce, cf. my R-devel post in thread
'Argument "nomatch" matched by multiple actual arguments ...
%in% -> match?!?' on March 6, 2008. Thanks Ran Pang for
reminding me and for additional troubleshooting.
o Added support for more "short tags" in the Rdoc compiler.
Version: 1.4.5 [2008-05-28]
o SPELL CORRECTION: Added getInstantiationTime(), but keeping
misspelled (and now deprecated) getInstanciationTime() for backward
compatibility. The internal attribute was also renamed, but the
above method look for both in case saved objects are loaded.
Version: 1.4.4 [2008-05-08]
o Added getNews() and showNews() to the Package class. NEWS files
are now detected (first).
o Added getConstructorS3().
o The NEWS file does now replace the former HISTORY file of R.oo.
o If running R v2.7.0 or new, the first element of vector 'ASCII'
is an empty string. This is because ASCII 0x00 cannot be represented
as an R string and in R v2.8.0 it will give a warning. Note though
that regardless of this, charToInt(intToChar(0)) == 0 is still TRUE.
Version: 1.4.3 [2008-03-25]
o BUG FIX: getInternalAddress() would return NA.
o Added getName() for environment:s.
Version: 1.4.2 [2008-03-06]
o Added paper to citation("R.oo").
o BUG FIX: Regular expression pattern 'a-Z' is illegal on (at least)
some locale, e.g. 'C' (where 'A-z' works). The only way to specify
the ASCII alphabet is to list all characters explicitly, which we now
do in all methods of the package. See the r-devel thread
"invalid regular expression '[a-Z]'" on 2008-03-05 for details.
Version: 1.4.1 [2008-01-10]
o Made the registered finalizer calling finalize() more error prone.
Version: 1.4.0 [2007-09-17]
o Extracted setMethodS3() and related methods from R.oo and put them
in a standalone R.methodsS3 package. While doing this, the
'enforceRCC' argument used by setMethodS3() was renamed to 'validators'
which now takes an optional list of functions. Any code using
argument 'enforceRCC=FALSE' must now use 'validators=NULL'.
o CLEAN UP: Removed code that patched R v1.8.0 and before.
Version: 1.3.0 [2007-08-29]
o Now the startup message when loading the package is generated with
packageStartupMessage() so that it can be suppressed.
o CLEAN UP: Removed showAndWait() for simpleError, which displayed
a TclTk dialog for a generic error. Never used. If someone wants
the code, please tell me and I'll forward it.
o CLEAN UP: Removed deprecated trycatch(); use tryCatch() instead.
o CLEAN UP: Removed patched for R v1.8.x and before: stop(), try().
o BUG FIX: If Object:s are garbage collected after R.oo has been detached,
the error 'Error in function (env) : could not find function "finalize"'
would be thrown, because the registered finalizer hook tries to call
the generic function finalize() in R.oo. We solve this by trying to
reload R.oo (and the unload it again). Special care was taken so that
Object:s allocated by R.oo itself won't cause an endless loop.
Version: 1.2.8 [2007-06-09]
o Removed (incorrect) argument name 'list' from all substitute() calls.
o Removed already deprecated getData() because there might be a name
clash with the 'nlme' package.
o BUG FIX: Queried non-existing object 'error' instead of 'ex' in
the exception handling of update() of the Package class.
Version: 1.2.7 [2007-04-07]
o Removed support for R v2.0.0 and before.
o Removed reportBug() since it was never completed.
Version: 1.2.6 [2007-03-24]
o Now ll() uses objectSize() instead of object.size(). It also
returns the properties in its "minimal" data type, e.g. the
'objectSize' column contains integers (not characters as before).
This makes it possible to utilize subset() on the ll() output.
o Added a default method for objectSize(), which is just a wrapper
for object.size().
o Made trycatch() defunct, i.e. it gives an error suggesting to use
tryCatch() instead.
Version: 1.2.5 [2007-01-05]
o BUG FIX: getMethods(..., private=FALSE) for class Class would return
private methods, and private=TRUE would remove them. It should be
the other way around.
o BUG FIX: getMethods() for Class would sometimes give error message:
"Error in result[[k]] : subscript out of bounds". This in turn would
cause Rdoc to fail.
Version: 1.2.4 [2006-10-03]
o BUG FIX: Since getInternalAddress() coerced the address to an integer,
addresses about 2^32 bytes = 4GB got address NA. Now
getInternalAddress() and the default hashCode() return a double.
Version: 1.2.3 [2006-09-07]
o Added package 'utils' as a package this one depends on. This
is required for package without a namespace in the upcoming
R v2.4.0 release.
o Removed deprecated method getClass() for class Object but also
BasicObject. These were deprecated on 2002-12-15.
Version: 1.2.2 [2006-08-11]
o Added support for give modifiers to fields in classes extending
the Object class. Currently it is only the "cached" modifier that
is recognized. To specify that a field, say, "foo" is "cached",
list it as "cached:foo". Fields that are "cached" will be assigned
to NULL when clearCache() of the object is called. For convenience
there is also a
gc() method for all Object:s. See ?gc.Object for
an example.
o Made the package smaller by removing the DSC-2003 logo from
the R.oo paper, which shrunk from 324kb to 220kb. The rest
of the files in the source distribution is about 80kb when
gzipped, i.e. still the paper is three times larger than the
rest of the package.
Version: 1.2.0 [2006-07-14]
o BUG FIX: update(R.oo) would throw an error and the package was
detached.
Version: 1.1.9 [2006-06-14]
o Added method getEnvironment() to class Object, which will return
the environment where the Object's members are stored.
o Now ll() does not assign variables in the lookup environment, which
means it will work with sealed environments too.
Version: 1.1.8 [2006-05-30]
o Added isBeingCreated() to Class in order to check if the constructor
was called to create the static instance or just any instance.
o Removed setClassS3() which has been deprecated since 2003(!).
o Now the Rdoc tag @allmethods takes an optional argument specifying
if private, protected or public methods should be listed.
Version: 1.1.7 [2006-05-22]
o Added argument 'addTimestamp=TRUE' to Rdoc$compile(). This makes it
possible to turn of the timestamp, because timestamps makes diff,
say the one in Subversion, think there is a real different.
o BUG FIX: Rdoc$compile() did not write the name of the source file
in the header (anymore).
o BUG FIX: The code for automatic formatting of replacement methods
generated an error.
Version: 1.1.6 [2006-04-03]
o This version was commited to CRAN.
o Now the Rdoc compiler recognizes replacement functions and
creates the correct Rd \usage{} format for these.
Version: 1.1.5 [2006-03-28]
o Now argument 'properties' of ll() is given by the option
"R.oo::ll/properties". If not set when the package is loaded,
it is set to a default value. See help(ll) for more details. This
was suggested by Tim Beissbarth, German Cancer Research Center.
o BUG FIX: showHistory() for the Package class was calling itself.
o BUG FIX: Compiling Rdoc comments with invalid keyword tags would
generate an internal error. Same for invalid visibility tags etc.
Version: 1.1.4 [2006-02-18]
o Now the Rdoc compiler also escapes Rd filenames for @see and
@seemethod tags.
Version: 1.1.3 [2006-02-09]
o Removed all usage of NULL environments since they are now
deprecated in R v2.3.0.
o Added getChangeLog() and showChangeLog() to the Package class.
The get- and showHistory(), which are to be made deprecated in
the future, are now wrappers for these two methods.
o Added Rdoc tag @RdocPackage to generate -package.Rd files.
o Now the Rdoc compiler makes sure that the generated Rd files
all starts with a letter or a digit. If not, it adds a
default prefix (currently "000"). If not, the new R v2.3.0
R CMD check may complaint about missing objects.
o Now '...' is added explicitly to setMethodS3() in all Rd examples.
Version: 1.1.2 [2006-01-06]
o Added Rd links to classes listed under "Directly known subclasses:".
Version: 1.1.1 [2005-11-23]
o Added validation of arguments in replacement functions.
o Added RCC validation of arguments in 'picky' methods, e.g. $()".
o BUG FIX: The "$(), field, static field etc.
When a "match" found and the value was assigned, it did not return
(except for the set() match), but instead contiued search for
the rest. One effect of this was that the new value was always assign
to the static field too. The fix make the code run faster too.
Thanks Edouard Duchesnay at Service Hospitalier Frédéric Joliot,
Commissariat à l'Energie Atomique, France for spotting this.
Version: 1.1.0 [2005-07-18]
o BUG FIX: Rdoc$compile() sometimes generated the error "invalid regular
expression '\name{[^\}]*}'" (forgot to escape '{' and '}'). Fixed.
Thanks Lorenz Wernisch, School of Crystallography, University of London
of reporting this.
o BUG FIX: getDetails() in Class would list private and protected methods
as public.
o BUG FIX: Argument 'enforceRCC' of setMethodS3() was not passed to
setGenericS3().
o Added a section on "Defining static fields" to the help page of Object.
o Added argument 'replaceNewline' to getDescription() of Package.
o Now as.character() of Package reports the title, the license, and the
description, but no longer if the package is part of a bundle. The
latter was too slow since it had to scan all installed packages.
o Now print() of Class passes '...' to getDetails(), that is, now
print(Class, private=TRUE) will work too.
o Added attachLocally() to the Object class.
o Added extend.default(), which can be used to extend any type of object.
o Now pure Object:s are also finalized. Before only subclasses defined
via extend(, "", ...) was finalized. This was not a
big deal, because the finalize():er of the Object class is empty anyway.
Version: 1.0.5 [2005-06-03]
o Now the static load() method in Object asserts that the loaded Object
inherits from the class that the static object, which is used to call
load(), is of. Thus, Object$load(...) will load all Object:s, whereas
MyClass$load(...) will only load objects inheriting from MyClass.
o Rdoc compiler:
- Now an RdocMethod tag will not add keyword 'internal' if the class
starts with a lower case, e.g. 'matrix'.
- A '@keyword foo' can now be removed with '@keyword -foo'. Order
is irrelevant, since @keyword:s are added at the very end.
Version: 1.0.4 [2005-05-02]
o Added getDevelUrl() to the Package class.
Version: 1.0.3 [2005-02-28]
o Argument 'appendVarArgs' of setMethodS3() is now ignored if
a replacement function (named "nnn". Found a way
(ad hoc?) to get rid of them. See source code for details.
This should remove similar warnings from packages loading R.oo.
Version: 1.0.1 [2005-02-20]
o Package now outputs "See ?R.oo for help" when loaded.
o Now using three-digit version numbers, e.g. a.b.c where
a,b,c in 0,1,...,9. 'a' is updated for major updates,
'b' for minor updates and 'c' is for minor revisions.
o Removed require(methods) for R v2.0.0 and above.
o setMethodS3(..., abstract=TRUE) now defines abstract methods
with '...' as the only argument(s).
Version: 1.00 [2005-02-15]
o Moved to CRAN.
Version: 0.70 [2005-02-15]
o Package now passes R CMD check on R v2.1.0 devel without warnings.
o Added appendVarArgs=TRUE to setMethodS3(), which specifies that
'...' should be added, if missing.
o Add argument '...' to all methods to make it even more consistent
with any generic function. This is also done for a few methods
in the R base packages.
Version: 0.69 [2005-02-11]
o Package now passes R CMD check on R v2.1.0 devel also.
Had do modify a few lines of code to meet the new stricter regular
expression patterns.
o Renamed get- & showDescription() to get- & showDescriptionFile() and
added getDescription() to get the 'Description' field of DESCRIPTION.
o Moving away from trycatch() in favor of tryCatch().
trycatch() remains for a while, but will be made deprecated
in future version and later probably defunct.
o Added an example to setMethodS3() that is not using Object().
Version: 0.68 [2005-02-09]
o By default, now Rdoc$compile() runs Rdoc$check() at the end.
o Rdoc: Added a first simple test for undefined top-level tags in
the generated Rd code. Utilizes tools::Rd_parse(), which might
be renamed etc. according to its help page.
o Tag-variables such as @author now search for value in options() too.
Version: 0.67 [2004-10-23]
o BUG FIX: getRdMethods() in Class returned empty \tabular{rll}{}
if no methods exist, but this gives an error in R CMD Rdconv.
Version: 0.66 [2004-10-21]
o When using setMethodS3(..., abstract=TRUE) in a package that
uses lazy loading, which all new packages do by default,
warnings like "using .GlobalEnv instead of package:utils" will
be generated the first time the abstract method is accessed.
This is because eval() is used to create the abstract method;
we are looking for a way that will not generate these warnings,
although they are not serious.
Example: library(R.colors); print(getColorSpace.Color)
o Made the package compatible with R v2.0.0 too. Had to move example
file 'Exception.R' from data/ to inst/misc/ and update the help
example for Rdoc. Update the example of unload() for the Package
class to load the 'boot' package instead of obsolete 'ts'.
o Added help to more methods.
o Added getEnvironment() to the Package class.
o BUG FIX: Rdoc tags was not be parsed by the Rdoc compiler for
deprecated methods.
Version: 0.65 [2004-06-27]
o Substantially improved the loading of all my packages. The Package()
constructor, which was called when a new package was loaded, was slow
unnecessarily slow because of an internal call to installed.packages().
o BUG FIX: getInternalAddress() for class Object was "too" hard coded
making it not work correctly on for instance Suse Linux. Assumed fixed
positions of the hexadecimal address of the environment. Now a gsub()
with a backreference is used. Should be more safe.
o Added known generic function 'as.vector()'.
o Added documentation to many methods.
Version: 0.64 [2004-04-21]
o Fixed deprecated warning about package.description() that
occured R v1.9.0 such that the code still works for older
versions of R. This was needed for the Package class.
Version: 0.63 [2004-03-03]
o To anyone using setClassS3(), please use setConstructorS3() instead;
setClassS3() is deprecated and will be phased out soon!
o Updated trycatch() (and the Exception class) to work with R v1.8.1.
If running R v1.8.1, then tryCatch() is used internally. For R v1.7.1
and before the old trycatch() is used, which will be made deprecated
later on. Added a throw() for the error class too for rethrowing errors.
o Update the Rdoc compiler to generate correct \name and \alias Rd tags.
o BUG FIX: Package class - from R v1.8.1 we noted that R CMD check made
installed.packages() return multiple matches of the same package. This
might have been a problem before too, but R CMD check never complained.
Version: 0.62 [2003-12-31]
o Added an "about" section in the documentation.
o Added showDescription(), getHistory(), showHistory(), getHowToCite()
and showHowToCite() to the Package class.
o BUG FIX: For some Rdoc types the \keyword{} statement was placed on
the same line as the previous Rd statement. This sometimes generated
cluttered Rd index files.
Version: 0.61 [2003-12-16]
o Package: update() does now also reload the updated package by default.
o Exception: Now the throw() method includes the complete stacktrace
too when generating a error signal. In other words, the user will
automatically see the stacktrace of the error if the error is not
caught. Same for stop().
o Rdoc: Added the tag @RdocDocumentation for general documentation.
Version: 0.60 [2003-10-28]
o BUG FIX: "$ and set,
which is done by using substr() "cf."
o BUG FIX: getStaticInstance() of class Class did not recover correctly
if static instance was missing.
Version: 0.51 [2003-01-17]
o Added getUrl(), getMaintainer(), getAuthor(), getTitle(), getLicense()
and getBundle(). Made the output from as.character() more informative.
o Added a caching feature of "$"() to speed up access to members. The
first time a member (field, virtual field, static field, method etc) is
accessed it is done by looking it up one at the time and taking the
first existing one (in a predefined order). The second time the same
field is accessed, the name is remembered and "$"() access the right
member directly. If this works out, "$() idea as described below.
Maybe a "[()" exists, the value of
get() is returned. This way one can have fields that
are generated "on the fly" to save memory etc. This new feature required
that "[[".Object was modified (actually created).
Example: For an object 'obj' one can get its class by either the
classical getClass(obj) or by the new feature obj$Class.
If this new feature are successful, I will also look at implementing a
corresponding set() support.
o BUG FIX: setGenericS3() gave an error if one tried to set a generic
function with the same name as an [R] object that was *not* a function.
A simple add of argument mode="function" to the exists() check fixed this.
Version: 0.38 [2002-04-02]
o BUG FIX: clone() in class Reference did not work properly; it gave the
wrong internal reference names, which in turn would generate errors such
as 'Error in get(x, envir, mode, inherits) : variable "Reference.METHODS"
was not found' when one tried object$foo() instead of foo(object). Now
it works again.
Version: 0.37 [2002-03-30]
o IMPROVEMENT: Since library(methods) might be loaded after library(R.oo)
the function extends() breaks down. Worked this out a little bit by
detaching and reloading R.oo in function createClass() if it is detected
that extends() has changed.
o IMPROVEMENT: Forces extends .methods.Rdoc, which
can be included in the Rdoc comments by @include ".methods.Rdoc".
Hopefully, this will mean that the list of methods in the help files
will be more up to date.
o Declared more internal methods as "private".
o BUG FIX: Internal scanForMethods() did not make a difference of functions
and non-functions, since it basically only looked at the name. For
instance would CONST.Foo